Numerous charged-based separation methods are available for use with biopolymers which bear a charge at neutral or near-neutral pH, such as nucleic acids and the majority of proteins. These include, for example, various modes of electrophoresis, isoelectric focusing, and ion exchange. Such methods, however, cannot generally be employed for substantially uncharged oligonucleotide analogs without prior ionization of the molecules. For example, current methods of ion exchange separation of uncharged oligonucleotides require ionization of the molecules at either high pH (>11), at which G and T bases ionize, or at low pH (<3), at which C and A bases ionize. Some uncharged oligonucleotide analogs, such as, for example, phosphoramidate- or phosphorodiamidate-linked oligomers, are not stable at these low pH's. Accordingly, there is a need for methods of separation of such uncharged molecules that can be can be carried out under mild conditions, at neutral or near neutral pH.